libSBML Python API
5.10.0
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{comp}
comp Implementation of the Port construct from the “comp” package.The Port class was introduced by the SBML Level 3 Hierarchical Model Composition package (“comp”) to allow a Model to define a standard interface between it and other models that might use it as a submodel. It derives from the SBaseRef class, and the elements defined there refer to elements in the same parent Model as the Port object. A Port object instance therefore uses those attributes to define a port for a component in a model. When other SBaseRef or SBaseRef-derived classes refer to a Port object using a 'portRef' attribute, the element being referenced is the element the Port object itself points to.
In the present formulation of the Hierarchical Model Composition package, the use of ports is not enforced, nor is there any mechanism to restrict which ports may be used in what ways—they are only an advisory construct. Future versions of this SBML package may provide additional functionality to support explicit restrictions on port use. For the present definition of Hierarchical Model Composition, users of models containing ports are encouraged to respect the modeler's intention in defining ports, and use the port definitions to interact with components through their ports (when they have ports defined) rather than interact directly with the components.
The required attribute 'id' is used to give an identifier to a Port object so that other objects can refer to it. The attribute has type PortSId and is essentially identical to the SBML primitive type SId, except that its namespace is limited to the identifiers of Port objects defined within a Model object. In parallel, the PortSId type has a companion type, PortSIdRef, that corresponds to the SBML primitive type SIdRef; the value space of PortSIdRef is limited to PortSId values.
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Python method signature(s):
addCVTerm(SBase self, CVTerm term, bool newBag=False)int addCVTerm(SBase self, CVTerm term)
int
Adds a copy of the given CVTerm object to this SBML object.
term | the CVTerm to assign. |
newBag | if True , creates a new RDF bag with the same identifier as a previous bag, and if False , adds the term to an existing RDF bag with the same type of qualifier as the term being added. |
create
) for alternatives that do not lead to these issues.
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Python method signature(s):
appendAnnotation(SBase self, XMLNode annotation)int appendAnnotation(SBase self, string annotation)
int
This method has multiple variants that differ in the arguments they accept. Each is described separately below.
appendAnnotation(XMLNode annotation)
Appends the given annotation
to the 'annotation' subelement of this object.
Whereas the SBase 'notes' subelement is a container for content to be shown directly to humans, the 'annotation' element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for 'annotation'. The element's content type is XML type 'any', allowing essentially arbitrary well-formed XML data content.
SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.
Unlike SBase.setAnnotation() or SBase.setAnnotation(), this method allows other annotations to be preserved when an application adds its own data.
annotation | an XML structure that is to be copied and appended to the content of the 'annotation' subelement of this object |
appendAnnotation(string annotation)
Appends the given annotation
to the 'annotation' subelement of this object.
Whereas the SBase 'notes' subelement is a container for content to be shown directly to humans, the 'annotation' element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for 'annotation'. The element's content type is XML type 'any', allowing essentially arbitrary well-formed XML data content.
SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.
Unlike SBase.setAnnotation() or SBase.setAnnotation(), this method allows other annotations to be preserved when an application adds its own data.
annotation | an XML string that is to be copied and appended to the content of the 'annotation' subelement of this object |
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Python method signature(s):
appendNotes(SBase self, XMLNode notes)int appendNotes(SBase self, string notes)
int
This method has multiple variants that differ in the arguments they accept. Each is described separately below.
appendNotes(string notes)
Appends the given notes
to the 'notes' subelement of this object.
The content of the parameter notes
is copied.
The optional SBML element named 'notes', present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.
The format of 'notes' elements must be XHTML 1.0. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker.hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and 3 specifications have considerable detail about how 'notes' element content must be structured.
notes | an XML string that is to appended to the content of the 'notes' subelement of this object |
appendNotes(XMLNode notes)
Appends the given notes
to the 'notes' subelement of this object.
The content of notes
is copied.
The optional SBML element named 'notes', present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.
The format of 'notes' elements must be XHTML 1.0. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker.hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and 3 specifications have considerable detail about how 'notes' element content must be structured.
notes | an XML node structure that is to appended to the content of the 'notes' subelement of this object |
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Python method signature(s):
clearReferencedElement(SBaseRef self)
Removes the saved referenced element, if it had been saved earlier.
def libsbml.Port.clone | ( | self | ) |
{comp}
comp Implementation of the Port construct from the “comp” package.The Port class was introduced by the SBML Level 3 Hierarchical Model Composition package (“comp”) to allow a Model to define a standard interface between it and other models that might use it as a submodel. It derives from the SBaseRef class, and the elements defined there refer to elements in the same parent Model as the Port object. A Port object instance therefore uses those attributes to define a port for a component in a model. When other SBaseRef or SBaseRef-derived classes refer to a Port object using a 'portRef' attribute, the element being referenced is the element the Port object itself points to.
In the present formulation of the Hierarchical Model Composition package, the use of ports is not enforced, nor is there any mechanism to restrict which ports may be used in what ways—they are only an advisory construct. Future versions of this SBML package may provide additional functionality to support explicit restrictions on port use. For the present definition of Hierarchical Model Composition, users of models containing ports are encouraged to respect the modeler's intention in defining ports, and use the port definitions to interact with components through their ports (when they have ports defined) rather than interact directly with the components.
The required attribute 'id' is used to give an identifier to a Port object so that other objects can refer to it. The attribute has type PortSId and is essentially identical to the SBML primitive type SId, except that its namespace is limited to the identifiers of Port objects defined within a Model object. In parallel, the PortSId type has a companion type, PortSIdRef, that corresponds to the SBML primitive type SIdRef; the value space of PortSIdRef is limited to PortSId values. Python method signature(s):
clone(Port self)Port
Creates and returns a deep copy of this Port object.
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Python method signature(s):
disablePackage(SBase self, string pkgURI, string pkgPrefix)int
Disables the given SBML Level 3 package on this object.
This method disables the specified package on this object and other objects connected by child-parent links in the same SBMLDocument object.
An example of when this may be useful is during construction of model components when mixing existing and new models. Suppose your application read an SBML document containing a model that used the SBML Hierarchical Model Composition (“comp”) package, and extracted parts of that model in order to construct a new model in memory. The new, in-memory model will not accept a component drawn from another SBMLDocument with different package namespace declarations. You could reconstruct the same namespaces in the in-memory model first, but as a shortcut, you could also disable the package namespace on the object being added. Here is a code example to help clarify this:
import sys import os.path from libsbml import * # We read in an SBML L3V1 model that uses the 'comp' package namespace doc = readSBML('sbml-file-with-comp-elements.xml'); # We extract one of the species from the model we just read in. s1 = doc.getModel().getSpecies(0); # We construct a new model. This model does not use the 'comp' package. newDoc = SBMLDocument(3, 1); newModel = newDoc.createModel(); # The following would fail with an error, because addSpecies() would # first check that the parent of the given object has namespaces # declared, and will discover that s1 does but newModel does not. # newModel.addSpecies(s1); # However, if we disable the 'comp' package on s1, then the call # to addSpecies will work. s1.disablePackage('http://www.sbml.org/sbml/level3/version1/comp/version1', 'comp'); newModel.addSpecies(s1);
pkgURI | the URI of the package |
pkgPrefix | the XML prefix of the package |
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Python method signature(s):
enablePackage(SBase self, string pkgURI, string pkgPrefix, bool flag)int
Enables or disables the given SBML Level 3 package on this object.
This method enables the specified package on this object and other objects connected by child-parent links in the same SBMLDocument object. This method is the converse of SBase.disablePackage().
pkgURI | the URI of the package. |
pkgPrefix | the XML prefix of the package |
flag | whether to enable (True ) or disable (False ) the package |
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Python method signature(s):
getAncestorOfType(SBase self, int type, string pkgName="core")SBase getAncestorOfType(SBase self, int type)
SBase getAncestorOfType(SBase self, int type, string pkgName="core")
SBase getAncestorOfType(SBase self, int type)
SBase
Returns the first ancestor object that has the given SBML type code from the given package.
LibSBML attaches an identifying code to every kind of SBML object. These are known as SBML type codes. In the Python language interface for libSBML, the type codes are defined as static integer constants in the interface class libsbml. The names of the type codes all begin with the characters SBML_
.
This method searches the tree of objects that are parents of this object, and returns the first one that has the given SBML type code from the given pkgName
.
type | the SBML type code of the object sought |
pkgName | (optional) the short name of an SBML Level 3 package to which the sought-after object must belong |
None
if no ancestor exists.pkgName
must be used for all type codes from SBML Level 3 packages. Otherwise, the function will search the 'core' namespace alone, not find any corresponding elements, and return None.
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Python method signature(s):
getAnnotation(SBase self)XMLNode getAnnotation(SBase self)
XMLNode
Returns the content of the 'annotation' subelement of this object as a tree of XMLNode objects.
SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.
The annotations returned by this method will be in XML form. LibSBML provides an object model and related interfaces for certain specific kinds of annotations, namely model history information and RDF content. See the ModelHistory, CVTerm and RDFAnnotationParser classes for more information about the facilities available.
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Python method signature(s):
getAnnotationString(SBase self)string getAnnotationString(SBase self)
string
Returns the content of the 'annotation' subelement of this object as a character string.
SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.
The annotations returned by this method will be in string form. See the method getAnnotation() for a version that returns annotations in XML form.
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Python method signature(s):
getColumn(SBase self)long
Returns the column number on which this object first appears in the XML representation of the SBML document.
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Python method signature(s):
getCVTerms()CVTermList
Get the CVTermList of CVTerm objects in this SBase.
Returns the CVTermList for this SBase.
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Python method signature(s):
getElementByMetaId(SBaseRef self, string metaid)SBase
Returns the first child element it can find with the given metaid
, or itself if it has the given metaid
, or None
if no such object is found.
metaid | string representing the metaid of objects to find |
metaid
.
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Python method signature(s):
getElementBySId(SBaseRef self, string id)SBase
Returns the first child element found that has the given id
in the model-wide SId namespace, or None
if no such object is found.
id | string representing the id of objects to find |
id
. def libsbml.Port.getElementName | ( | self | ) |
Python method signature(s):
getElementName(Port self)string
Returns the XML element name of this SBML object.
def libsbml.Port.getId | ( | self | ) |
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Python method signature(s):
getLevel(SBase self)long
Returns the SBML Level of the SBMLDocument object containing this object.
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Python method signature(s):
getLine(SBase self)long
Returns the line number on which this object first appears in the XML representation of the SBML document.
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Python method signature(s):
getListOfAllElementsFromPlugins(SBase self, ElementFilter filter=None)SBaseList getListOfAllElementsFromPlugins(SBase self)
SBaseList
Returns an SBaseList of all child SBase objects contained in SBML package plugins.
This method walks down the list of all packages used by the model and returns all objects contained in them.
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Python method signature(s):
getMetaId(SBase self)string
Returns the value of the 'metaid' attribute of this object.
ID
, the XML identifier type, which means each 'metaid' value must be globally unique within an SBML file. The latter point is important, because the uniqueness criterion applies across any attribute with type ID
anywhere in the file, not just the 'metaid' attribute used by SBML—something to be aware of if your application-specific XML content inside the 'annotation' subelement happens to use the XML ID
type. Although SBML itself specifies the use of XML ID
only for the 'metaid' attribute, SBML-compatible applications should be careful if they use XML ID
's in XML portions of a model that are not defined by SBML, such as in the application-specific content of the 'annotation' subelement. Finally, note that LibSBML does not provide an explicit XML ID
data type; it uses ordinary character strings, which is easier for applications to support.
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Python method signature(s):
getModelHistory(SBase self)ModelHistory getModelHistory(SBase self)
ModelHistory
Returns the ModelHistory object, if any, attached to this object.
None
if none exist.def libsbml.Port.getName | ( | self | ) |
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Python method signature(s):
getNamespaces(SBase self)XMLNamespaces
Returns a list of the XML Namespaces declared on this SBML document.
The SBMLNamespaces object encapsulates SBML Level/Version/namespaces information. It is used to communicate the SBML Level, Version, and (in Level 3) packages used in addition to SBML Level 3 Core.
None
in certain very usual circumstances where a namespace is not set.
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Python method signature(s):
getNotes(SBase self)XMLNode getNotes(SBase self)
XMLNode
Returns the content of the 'notes' subelement of this object as a tree of XMLNode objects.
The format of 'notes' elements conform to the definition of XHTML 1.0. However, the content cannot be entirely free-form; it must satisfy certain requirements defined in the SBML specifications for specific SBML Levels. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker.hasExpectedXHTMLSyntax(); The method implements a verification process that lets callers check whether the content of a given XMLNode object conforms to the SBML requirements for 'notes' and 'message' structure. Developers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations of using 'notes' in SBML. The SBML Level 2 and 3 specifications have considerable detail about how 'notes' element content must be structured.
The 'notes' element content returned by this method will be in XML form, but libSBML does not provide an object model specifically for the content of notes. Callers will need to traverse the XML tree structure using the facilities available on XMLNode and related objects. For an alternative method of accessing the notes, see getNotesString().
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Python method signature(s):
getNotesString(SBase self)string getNotesString(SBase self)
string
Returns the content of the 'notes' subelement of this object as a string.
The format of 'notes' elements conform to the definition of XHTML 1.0. However, the content cannot be entirely free-form; it must satisfy certain requirements defined in the SBML specifications for specific SBML Levels. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker.hasExpectedXHTMLSyntax(); The method implements a verification process that lets callers check whether the content of a given XMLNode object conforms to the SBML requirements for 'notes' and 'message' structure. Developers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations of using 'notes' in SBML. The SBML Level 2 and 3 specifications have considerable detail about how 'notes' element content must be structured.
For an alternative method of accessing the notes, see getNotes(), which returns the content as an XMLNode tree structure. Depending on an application's needs, one or the other method may be more convenient.
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Python method signature(s):
getNumPlugins(SBase self)long
Returns the number of plug-in objects (extenstion interfaces) for SBML Level 3 package extensions known.
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Python method signature(s):
getNumReferents(SBaseRef self)int
Returns how many elements are being referred to by this SBaseRef. A valid SBaseRef will have exactly one. Possible referents are portRef, idRef, unitRef, and metaIdRef.
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Python method signature(s):
getPackageName(CompBase self)string
Returns the package name of this plugin object.
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{comp}
comp A convenience subclass of “comp” package SBase-derived classesThe CompBase class derives from SBase, and defines a few functions and features common to all SBase-derived classes in the SBML Level 3 Hierarchical Model Composition package (“comp”). Python method signature(s):
getPackageURI(CompBase self)string
Returns the XML namespace (URI) of the package extension of this object.
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Python method signature(s):
getPackageVersion(CompBase self)long
Returns the package version of the package extension of this plugin object.
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Python method signature(s):
getParentSBMLObject(SBase self)SBase getParentSBMLObject(SBase self)
SBase
Returns the parent SBML object containing this object.
This returns the immediately-containing object. This method is convenient when holding an object nested inside other objects in an SBML model.
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Python method signature(s):
getPlugin(SBase self, string package)SBasePlugin getPlugin(SBase self, string package)
SBasePlugin getPlugin(SBase self, long n)
SBasePlugin getPlugin(SBase self, long n)
SBasePlugin
This method has multiple variants that differ in the arguments they accept. Each is described separately below.
getPlugin(long n)
Returns the nth plug-in object (extension interface) for an SBML Level 3 package extension.
n | the index of the plug-in to return |
getPlugin(string package)
Returns a plug-in object (extension interface) for an SBML Level 3 package extension with the given package name or URI.
package | the name or URI of the package |
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Python method signature(s):
getPrefix(SBase self)string
Returns the namespace prefix of this element.
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Python method signature(s):
getReferencedElement(SBaseRef self)SBase
Returns the object pointed to by this element. If that element was previously found and set with 'saveReferencedElement', that element is returned; otherwise, 'saveReferencedElement' is called first, and the found element is returned.
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Python method signature(s):
getResourceBiologicalQualifier(SBase self, string resource)long
Returns the MIRIAM biological qualifier associated with the given resource.
In MIRIAM, qualifiers are an optional means of indicating the relationship between a model component and its annotations. There are two broad kinds of annotations: model and biological. The latter kind is used to qualify the relationship between a model component and a biological entity which it represents. Examples of relationships include 'is' and 'has part', but many others are possible. MIRIAM defines numerous relationship qualifiers to enable different software tools to qualify biological annotations in the same standardized way. In libSBML, the MIRIAM controlled-vocabulary annotations on an SBML model element are represented using lists of CVTerm objects, and the the MIRIAM biological qualifiers are represented using valueswhose names begin with BQB_
in the interface class libsbml.
This method searches the controlled-vocabulary annotations (i.e., the list of CVTerm objects) on the present object, then out of those that have biological qualifiers, looks for an annotation to the given resource
. If such an annotation is found, it returns the type of biological qualifier associated with that resource as a valuewhose name begins with BQB_
from the interface class libsbml.
resource | string representing the resource; e.g., 'http://www.geneontology.org/#GO:0005892' . |
BQB_
constants defined in libsbml may be expanded in later libSBML releases, to match the values defined by MIRIAM at that later time.
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Python method signature(s):
getResourceModelQualifier(SBase self, string resource)long
Returns the MIRIAM model qualifier associated with the given resource.
In MIRIAM, qualifiers are an optional means of indicating the relationship between a model component and its annotations. There are two broad kinds of annotations: model and biological. The former kind is used to qualify the relationship between a model component and another modeling object. An example qualifier is 'isDerivedFrom', to indicate that a given component of the model is derived from the modeling object represented by the referenced resource. MIRIAM defines numerous relationship qualifiers to enable different software tools to qualify model annotations in the same standardized way. In libSBML, the MIRIAM controlled-vocabulary annotations on an SBML model element are represented using lists of CVTerm objects, and the the MIRIAM model qualifiers are represented using valueswhose names begin with BQM_
in the interface class libsbml.
This method method searches the controlled-vocabulary annotations (i.e., the list of CVTerm objects) on the present object, then out of those that have model qualifiers, looks for an annotation to the given resource
. If such an annotation is found, it returns the type of type of model qualifier associated with that resource as a valuewhose name begins with BQM_
from the interface class libsbml.
resource | string representing the resource; e.g., 'http://www.geneontology.org/#GO:0005892' . |
BQM_
constants defined in libsbml may be expanded in later libSBML releases, to match the values defined by MIRIAM at that later time.
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Python method signature(s):
getSBMLDocument(SBase self)SBMLDocument getSBMLDocument(SBase self)
SBMLDocument
Returns the SBMLDocument object containing this object instance.
This method allows the caller to obtain the SBMLDocument for the current object.
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Python method signature(s):
getSBOTerm(SBase self)int
Returns the integer portion of the value of the 'sboTerm' attribute of this object.
Beginning with SBML Level 2 Version 3, objects derived from SBase have an optional attribute named 'sboTerm' for supporting the use of the Systems Biology Ontology. In SBML proper, the data type of the attribute is a string of the form 'SBO:NNNNNNN', where 'NNNNNNN' is a seven digit integer number; libSBML simplifies the representation by only storing the 'NNNNNNN' integer portion. Thus, in libSBML, the 'sboTerm' attribute on SBase has data type int
, and SBO identifiers are stored simply as integers. (For convenience, libSBML offers methods for returning both the integer form and a text-string form of the SBO identifier.)
SBO terms are a type of optional annotation, and each different class of SBML object derived from SBase imposes its own requirements about the values permitted for 'sboTerm'. Please consult the SBML Level 2 Version 4 specification for more information about the use of SBO and the 'sboTerm' attribute.
-1
if the value is not set.
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Python method signature(s):
getSBOTermAsURL(SBase self)string
Returns the identifiers.org URL representation of the 'sboTerm' attribute of this object.
This method returns the entire SBO identifier as a text string in the form 'http://identifiers.org/biomodels.sbo/SBO:NNNNNNN'.
SBO terms are a type of optional annotation, and each different class of SBML object derived from SBase imposes its own requirements about the values permitted for 'sboTerm'. Please consult the SBML Level 2 Version 4 specification for more information about the use of SBO and the 'sboTerm' attribute.
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Python method signature(s):
getSBOTermID(SBase self)string
Returns the string representation of the 'sboTerm' attribute of this object.
Beginning with SBML Level 2 Version 3, objects derived from SBase have an optional attribute named 'sboTerm' for supporting the use of the Systems Biology Ontology. In SBML proper, the data type of the attribute is a string of the form 'SBO:NNNNNNN', where 'NNNNNNN' is a seven digit integer number; libSBML simplifies the representation by only storing the 'NNNNNNN' integer portion. Thus, in libSBML, the 'sboTerm' attribute on SBase has data type int
, and SBO identifiers are stored simply as integers. This method returns the entire SBO identifier as a text string in the form 'SBO:NNNNNNN'.
SBO terms are a type of optional annotation, and each different class of SBML object derived from SBase imposes its own requirements about the values permitted for 'sboTerm'. Please consult the SBML Level 2 Version 4 specification for more information about the use of SBO and the 'sboTerm' attribute.
def libsbml.Port.getTypeCode | ( | self | ) |
Python method signature(s):
getTypeCode(Port self)int
Returns the libSBML type code of this object instance.
SBML_
”. In the Python language interface for libSBML, the type codes are defined as static integer constants in the interface class libsbml. Note that different Level 3 package plug-ins may use overlapping type codes; to identify the package to which a given object belongs, call the getPackageName()
method on the object.
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Python method signature(s):
getURI(SBase self)string
Gets the namespace URI to which this element belongs to.
For example, all elements that belong to SBML Level 3 Version 1 Core must would have the URI 'http://www.sbml.org/sbml/level3/version1/core'; all elements that belong to Layout Extension Version 1 for SBML Level 3 Version 1 Core must would have the URI 'http://www.sbml.org/sbml/level3/version1/layout/version1/'
This function first returns the URI for this element by looking into the SBMLNamespaces object of the document with the its package name. If not found, it willreturn the XML namespace to which this element belongs.
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Python method signature(s):
getVersion(SBase self)long
Returns the Version within the SBML Level of the SBMLDocument object containing this object.
def libsbml.Port.hasRequiredAttributes | ( | self | ) |
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Python method signature(s):
hasValidLevelVersionNamespaceCombination(SBase self)bool
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Python method signature(s):
isPackageEnabled(SBase self, string pkgName)bool
Predicate returning True
if the given SBML Level 3 package is enabled with this object.
The search ignores the package version.
pkgName | the name of the package |
True
if the given package is enabled within this object, false
otherwise.
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Python method signature(s):
isPackageURIEnabled(SBase self, string pkgURI)bool
Predicate returning True
if an SBML Level 3 package with the given URI is enabled with this object.
pkgURI | the URI of the package |
True
if the given package is enabled within this object, false
otherwise.
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Python method signature(s):
isPkgEnabled(SBase self, string pkgName)bool
Predicate returning True
if the given SBML Level 3 package is enabled with this object.
The search ignores the package version.
pkgName | the name of the package |
True
if the given package is enabled within this object, false
otherwise.
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Python method signature(s):
isPkgURIEnabled(SBase self, string pkgURI)bool
Predicate returning True
if an SBML Level 3 package with the given URI is enabled with this object.
pkgURI | the URI of the package |
True
if the given package is enabled within this object, false
otherwise.
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Python method signature(s):
isSetAnnotation(SBase self)bool
Predicate returning True
if this object's 'annotation' subelement exists and has content.
Whereas the SBase 'notes' subelement is a container for content to be shown directly to humans, the 'annotation' element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for 'annotation'. The element's content type is XML type 'any', allowing essentially arbitrary well-formed XML data content.
SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.
True
if a 'annotation' subelement exists, False
otherwise.def libsbml.Port.isSetId | ( | self | ) |
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inherited |
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inherited |
Python method signature(s):
isSetMetaId(SBase self)bool
Predicate returning True
if this object's 'metaid' attribute is set.
ID
, the XML identifier type, which means each 'metaid' value must be globally unique within an SBML file. The latter point is important, because the uniqueness criterion applies across any attribute with type ID
anywhere in the file, not just the 'metaid' attribute used by SBML—something to be aware of if your application-specific XML content inside the 'annotation' subelement happens to use the XML ID
type. Although SBML itself specifies the use of XML ID
only for the 'metaid' attribute, SBML-compatible applications should be careful if they use XML ID
's in XML portions of a model that are not defined by SBML, such as in the application-specific content of the 'annotation' subelement. Finally, note that LibSBML does not provide an explicit XML ID
data type; it uses ordinary character strings, which is easier for applications to support.True
if the 'metaid' attribute of this SBML object is set, False
otherwise.
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inherited |
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Python method signature(s):
isSetModelHistory(SBase self)bool
Predicate returning True
if this object has a ModelHistory object attached to it.
True
if the ModelHistory of this object is set, false
otherwise.def libsbml.Port.isSetName | ( | self | ) |
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inherited |
Python method signature(s):
isSetNotes(SBase self)bool
Predicate returning True
if this object's 'notes' subelement exists and has content.
The optional SBML element named 'notes', present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.
The format of 'notes' elements must be XHTML 1.0. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker.hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and 3 specifications have considerable detail about how 'notes' element content must be structured.
True
if a 'notes' subelement exists, False
otherwise.
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inherited |
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inherited |
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inherited |
Python method signature(s):
isSetSBOTerm(SBase self)bool
Predicate returning True
if this object's 'sboTerm' attribute is set.
True
if the 'sboTerm' attribute of this SBML object is set, False
otherwise.
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inherited |
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inherited |
Python method signature(s):
matchesRequiredSBMLNamespacesForAddition(SBase self, SBase sb)bool matchesRequiredSBMLNamespacesForAddition(SBase self, SBase sb)
bool
Returns True
if this object's set of XML namespaces are a subset of the given object's XML namespaces.
sb | an object to compare with respect to namespaces |
True
if this object's collection of namespaces is a subset of sb's
, False
otherwise.
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inherited |
Python method signature(s):
matchesSBMLNamespaces(SBase self, SBase sb)bool matchesSBMLNamespaces(SBase self, SBase sb)
bool
Returns True
if this object's set of XML namespaces are the same as the given object's XML namespaces.
sb | an object to compare with respect to namespaces |
True
if this object's collection of namespaces is the same as sb's
, False
otherwise.
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inherited |
Python method signature(s):
performDeletion(SBaseRef self)int
DEPRECATED FUNCTION: DO NOT USE
Deletes the referenced object, plus any other elements that element points to through ReplacedElement or ReplacedBy children. Instead of calling this function directly, use 'CompModelPlugin::instantiateSubmodels' instead, which deals with all the intricacies of replacements and deletions, and gives you access to the non-flattened hierarchical form of the model.
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Python method signature(s):
removeTopLevelAnnotationElement(SBase self, string elementName, string elementURI="", bool removeEmpty=True)int removeTopLevelAnnotationElement(SBase self, string elementName, string elementURI="")
int removeTopLevelAnnotationElement(SBase self, string elementName)
int
Removes the top-level element within the 'annotation' subelement of this SBML object with the given name and optional URI.
SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.
Calling this method allows a particular annotation element to be removed whilst the remaining annotations remain intact.
elementName | a string representing the name of the top level annotation element that is to be removed |
elementURI | an optional string that is used to check both the name and URI of the top level element to be removed |
removeEmpty | if after removing of the element, the annotation is empty, and the removeEmpty argument is true, the annotation node will be deleted (default). |
def libsbml.Port.renameMetaIdRefs | ( | self, | |
args | |||
) |
Python method signature(s):
renameMetaIdRefs(Port self, string oldid, string newid)
Renames the metaIdRef attribute on this element if the oldid matches.
def libsbml.Port.renameSIdRefs | ( | self, | |
args | |||
) |
Python method signature(s):
renameSIdRefs(Port self, string oldid, string newid)
Renames the idRef attribute on this element if the oldid matches.
def libsbml.Port.renameUnitSIdRefs | ( | self, | |
args | |||
) |
Python method signature(s):
renameUnitSIdRefs(Port self, string oldid, string newid)
Renames the unitRef attribute on this element if the oldid matches.
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inherited |
Python method signature(s):
replaceTopLevelAnnotationElement(SBase self, XMLNode annotation)int replaceTopLevelAnnotationElement(SBase self, string annotation)
int
This method has multiple variants that differ in the arguments they accept. Each is described separately below.
replaceTopLevelAnnotationElement(XMLNode annotation)
Replaces the given top-level element within the 'annotation' subelement of this SBML object and with the annotation element supplied.
SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.
This method determines the name of the element to be replaced from the annotation argument. Functionally it is equivalent to calling removeTopLevelAnnotationElement(name)
followed by calling appendAnnotation(annotation_with_name)
, with the exception that the placement of the annotation element remains the same.
annotation | XMLNode representing the replacement top level annotation |
replaceTopLevelAnnotationElement(string annotation)
Replaces the given top-level element within the 'annotation' subelement of this SBML object and with the annotation element supplied.
SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.
This method determines the name of the element to be replaced from the annotation argument. Functionally it is equivalent to calling removeTopLevelAnnotationElement(name)
followed by calling appendAnnotation(annotation_with_name)
, with the exception that the placement of the annotation element remains the same.
annotation | string representing the replacement top level annotation |
def libsbml.Port.saveReferencedElement | ( | self | ) |
Python method signature(s):
saveReferencedElement(Port self)int
Finds and stores the referenced object by finding its Model parent, calling 'getReferencedElementFrom()' on that model, and storing the result.
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inherited |
Python method signature(s):
setAnnotation(SBase self, XMLNode annotation)int setAnnotation(SBase self, string annotation)
int
This method has multiple variants that differ in the arguments they accept. Each is described separately below.
setAnnotation(XMLNode annotation)
Sets the value of the 'annotation' subelement of this SBML object.
The content of annotation
is copied, and any previous content of this object's 'annotation' subelement is deleted.
Whereas the SBase 'notes' subelement is a container for content to be shown directly to humans, the 'annotation' element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for 'annotation'. The element's content type is XML type 'any', allowing essentially arbitrary well-formed XML data content.
SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.
Call this method will result in any existing content of the 'annotation' subelement to be discarded. Unless you have taken steps to first copy and reconstitute any existing annotations into the annotation
that is about to be assigned, it is likely that performing such wholesale replacement is unfriendly towards other software applications whose annotations are discarded. An alternative may be to use SBase.appendAnnotation() or SBase.appendAnnotation().
annotation | an XML structure that is to be used as the new content of the 'annotation' subelement of this object |
setAnnotation(string annotation)
Sets the value of the 'annotation' subelement of this SBML object.
The content of annotation
is copied, and any previous content of this object's 'annotation' subelement is deleted.
Whereas the SBase 'notes' subelement is a container for content to be shown directly to humans, the 'annotation' element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for 'annotation'. The element's content type is XML type 'any', allowing essentially arbitrary well-formed XML data content.
SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.
Call this method will result in any existing content of the 'annotation' subelement to be discarded. Unless you have taken steps to first copy and reconstitute any existing annotations into the annotation
that is about to be assigned, it is likely that performing such wholesale replacement is unfriendly towards other software applications whose annotations are discarded. An alternative may be to use SBase.appendAnnotation() or SBase.appendAnnotation().
annotation | an XML string that is to be used as the content of the 'annotation' subelement of this object |
def libsbml.Port.setId | ( | self, | |
args | |||
) |
Python method signature(s):
setId(Port self, string id)int
Sets the value of the 'id' attribute of this Port.
This method fails if the id
is not a valid syntax for an SId.
id | the identifier for the port |
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inherited |
Python method signature(s):
setIdRef(SBaseRef self, string id)int
Sets the value of the 'idRef' attribute of this SBaseRef.
This method fails if the id is not a valid syntax for an SIdRef (LIBSBML_INVALID_ATTRIBUTE_VALUE ), or if the SBaseRef already points to an element of the submodel using a different interface (LIBSBML_OPERATION_FAILED ). A sBaseRef must use exactly one method to point to a submodel element.
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inherited |
Python method signature(s):
setMetaId(SBase self, string metaid)int
Sets the value of the meta-identifier attribute of this object.
ID
, the XML identifier type, which means each 'metaid' value must be globally unique within an SBML file. The latter point is important, because the uniqueness criterion applies across any attribute with type ID
anywhere in the file, not just the 'metaid' attribute used by SBML—something to be aware of if your application-specific XML content inside the 'annotation' subelement happens to use the XML ID
type. Although SBML itself specifies the use of XML ID
only for the 'metaid' attribute, SBML-compatible applications should be careful if they use XML ID
's in XML portions of a model that are not defined by SBML, such as in the application-specific content of the 'annotation' subelement. Finally, note that LibSBML does not provide an explicit XML ID
data type; it uses ordinary character strings, which is easier for applications to support.The string metaid
is copied.
metaid | the identifier string to use as the value of the 'metaid' attribute |
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inherited |
Python method signature(s):
setMetaIdRef(SBaseRef self, string id)int
Sets the value of the 'metaIdRef' attribute of this SBaseRef.
This method fails if the id is not a valid syntax for an IDREF (LIBSBML_INVALID_ATTRIBUTE_VALUE ), or if the SBaseRef already points to an element of the submodel using a different interface (LIBSBML_OPERATION_FAILED ). An sBaseRef must use exactly one method to point to a submodel element.
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inherited |
Python method signature(s):
setModelHistory(SBase self, ModelHistory history)int
Sets the ModelHistory of this object.
The content of history
is copied, and this object's existing model history content is deleted.
history | ModelHistory of this object. |
def libsbml.Port.setName | ( | self, | |
args | |||
) |
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inherited |
Python method signature(s):
setNamespaces(SBase self, XMLNamespaces xmlns)int
Sets the namespaces relevant of this SBML object.
The content of xmlns
is copied, and this object's existing namespace content is deleted.
The SBMLNamespaces object encapsulates SBML Level/Version/namespaces information. It is used to communicate the SBML Level, Version, and (in Level 3) packages used in addition to SBML Level 3 Core.
xmlns | the namespaces to set |
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inherited |
Python method signature(s):
setNotes(SBase self, XMLNode notes)int setNotes(SBase self, string notes, bool addXHTMLMarkup=False)
int setNotes(SBase self, string notes)
int
This method has multiple variants that differ in the arguments they accept. Each is described separately below.
setNotes(string notes, bool addXHTMLMarkup = false)
Sets the value of the 'notes' subelement of this SBML object to a copy of the string notes
.
The content of notes
is copied, and any existing content of this object's 'notes' subelement is deleted.
The optional SBML element named 'notes', present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.
The format of 'notes' elements must be XHTML 1.0. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker.hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and 3 specifications have considerable detail about how 'notes' element content must be structured.
The following code illustrates a very simple way of setting the notes using this method. Here, the object being annotated is the whole SBML document, but that is for illustration purposes only; you could of course use this same approach to annotate any other SBML component.
notes | an XML string that is to be used as the content of the 'notes' subelement of this object |
addXHTMLMarkup | a boolean indicating whether to wrap the contents of the notes argument with XHTML paragraph (<p> ) tags. This is appropriate when the string in notes does not already containg the appropriate XHTML markup. |
setNotes(XMLNode notes)
Sets the value of the 'notes' subelement of this SBML object.
The content of notes
is copied, and any existing content of this object's 'notes' subelement is deleted.
The optional SBML element named 'notes', present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.
The format of 'notes' elements must be XHTML 1.0. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker.hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and 3 specifications have considerable detail about how 'notes' element content must be structured.
notes | an XML structure that is to be used as the content of the 'notes' subelement of this object |
def libsbml.Port.setPortRef | ( | self, | |
args | |||
) |
Python method signature(s):
setPortRef(Port self, string id)int
Overrides SBaseRef::setPortRef to always fail, because Port objects themselves cannot refer to model elements by PortSId.
id | the identifier to set for the port reference |
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inherited |
Python method signature(s):
setSBaseRef(SBaseRef self, SBaseRef sBaseRef)int
Sets the sBaseRef definition of this SBaseRef to a copy of the given SBaseRef object instance.
This method fails if the added sBaseRef does not match the level/version/package of the parent object or if the added sBaseRef cannot be copied.
sBaseRef | the SBaseRef object instance to use. |
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inherited |
Python method signature(s):
setSBOTerm(SBase self, int value)int setSBOTerm(SBase self, string sboid)
int
This method has multiple variants that differ in the arguments they accept. Each is described separately below.
setSBOTerm(int value)
Sets the value of the 'sboTerm' attribute.
Beginning with SBML Level 2 Version 3, objects derived from SBase have an optional attribute named 'sboTerm' for supporting the use of the Systems Biology Ontology. In SBML proper, the data type of the attribute is a string of the form 'SBO:NNNNNNN', where 'NNNNNNN' is a seven digit integer number; libSBML simplifies the representation by only storing the 'NNNNNNN' integer portion. Thus, in libSBML, the 'sboTerm' attribute on SBase has data type int
, and SBO identifiers are stored simply as integers.
SBO terms are a type of optional annotation, and each different class of SBML object derived from SBase imposes its own requirements about the values permitted for 'sboTerm'. Please consult the SBML Level 2 Version 4 specification for more information about the use of SBO and the 'sboTerm' attribute.
value | the NNNNNNN integer portion of the SBO identifier |
setSBOTerm(string &sboid)
Sets the value of the 'sboTerm' attribute by string.
Beginning with SBML Level 2 Version 3, objects derived from SBase have an optional attribute named 'sboTerm' for supporting the use of the Systems Biology Ontology. In SBML proper, the data type of the attribute is a string of the form 'SBO:NNNNNNN', where 'NNNNNNN' is a seven digit integer number; libSBML simplifies the representation by only storing the 'NNNNNNN' integer portion. Thus, in libSBML, the 'sboTerm' attribute on SBase has data type int
, and SBO identifiers are stored simply as integers. This method lets you set the value of 'sboTerm' as a complete string of the form 'SBO:NNNNNNN', whereas setSBOTerm(int value) allows you to set it using the integer form.
SBO terms are a type of optional annotation, and each different class of SBML object derived from SBase imposes its own requirements about the values permitted for 'sboTerm'. Please consult the SBML Level 2 Version 4 specification for more information about the use of SBO and the 'sboTerm' attribute.
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inherited |
Python method signature(s):
setUnitRef(SBaseRef self, string id)int
Sets the value of the 'unitRef' attribute of this SBaseRef.
This method fails if the id is not a valid syntax for a UnitSIdRef (LIBSBML_INVALID_ATTRIBUTE_VALUE ), or if the SBaseRef already points to an element of the submodel using a different interface (LIBSBML_OPERATION_FAILED ). A sBaseRef must use exactly one method to point to a submodel element.
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inherited |
Python method signature(s):
toSBML(SBase self)string *
Returns a string consisting of a partial SBML corresponding to just this object.
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inherited |
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inherited |
Python method signature(s):
unsetAnnotation(SBase self)int
Unsets the value of the 'annotation' subelement of this SBML object.
Whereas the SBase 'notes' subelement is a container for content to be shown directly to humans, the 'annotation' element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for 'annotation'. The element's content type is XML type 'any', allowing essentially arbitrary well-formed XML data content.
SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.
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inherited |
def libsbml.Port.unsetId | ( | self | ) |
|
inherited |
|
inherited |
Python method signature(s):
unsetMetaId(SBase self)int
Unsets the value of the 'metaid' attribute of this SBML object.
ID
, the XML identifier type, which means each 'metaid' value must be globally unique within an SBML file. The latter point is important, because the uniqueness criterion applies across any attribute with type ID
anywhere in the file, not just the 'metaid' attribute used by SBML—something to be aware of if your application-specific XML content inside the 'annotation' subelement happens to use the XML ID
type. Although SBML itself specifies the use of XML ID
only for the 'metaid' attribute, SBML-compatible applications should be careful if they use XML ID
's in XML portions of a model that are not defined by SBML, such as in the application-specific content of the 'annotation' subelement. Finally, note that LibSBML does not provide an explicit XML ID
data type; it uses ordinary character strings, which is easier for applications to support.
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inherited |
|
inherited |
Python method signature(s):
unsetModelHistory(SBase self)int
Unsets the ModelHistory object attached to this object.
def libsbml.Port.unsetName | ( | self | ) |
|
inherited |
Python method signature(s):
unsetNotes(SBase self)int
Unsets the value of the 'notes' subelement of this SBML object.
The optional SBML element named 'notes', present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.
The format of 'notes' elements must be XHTML 1.0. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker.hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and 3 specifications have considerable detail about how 'notes' element content must be structured.
|
inherited |
|
inherited |
|
inherited |
Python method signature(s):
unsetSBOTerm(SBase self)int
Unsets the value of the 'sboTerm' attribute of this SBML object.